Package: PoolTestR 0.2.0

PoolTestR: Prevalence and Regression for Pool-Tested (Group-Tested) Data

An easy-to-use tool for working with presence/absence tests on 'pooled' or 'grouped' samples. The primary application is for estimating prevalence of a marker in a population based on the results of tests on pooled specimens. This sampling method is often employed in surveillance of rare conditions in humans or animals (e.g. molecular xenomonitoring). The package was initially conceived as an R-based alternative to the molecular xenomonitoring software, 'PoolScreen' <https://sites.uab.edu/statgenetics/software/>. However, it goes further, allowing for estimates of prevalence to be adjusted for hierarchical sampling frames, and perform flexible mixed-effect regression analyses (McLure et al. Environmental Modelling and Software. <doi:10.1016/j.envsoft.2021.105158>). The package is currently in early stages, however more features are planned or in the works: e.g. adjustments for imperfect test specificity/sensitivity, functions for helping with optimal experimental design, and functions for spatial modelling.

Authors:Angus McLure [aut, cre], Caitlin Cherryh [ctb]

PoolTestR_0.2.0.tar.gz
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PoolTestR.pdf |PoolTestR.html
PoolTestR/json (API)
NEWS

# Install 'PoolTestR' in R:
install.packages('PoolTestR', repos = c('https://angusmclure.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/angusmclure/pooltestr/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

4.65 score 5 stars 7 scripts 175 downloads 1 mentions 6 exports 82 dependencies

Last updated 3 days agofrom:a5a814fd47. Checks:OK: 1 NOTE: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 18 2024
R-4.5-win-x86_64NOTENov 18 2024
R-4.5-linux-x86_64NOTENov 18 2024
R-4.4-win-x86_64NOTENov 18 2024
R-4.4-mac-x86_64NOTENov 18 2024
R-4.4-mac-aarch64NOTENov 18 2024
R-4.3-win-x86_64NOTENov 18 2024
R-4.3-mac-x86_64NOTENov 18 2024
R-4.3-mac-aarch64NOTENov 18 2024

Exports:getPrevalenceHierPoolPrevPoolLinkPoolPrevPoolRegPoolRegBayes

Dependencies:abindbackportsbayesplotBHbootbridgesamplingbrmsBrobdingnagcallrcheckmateclicodacodetoolscolorspacecrayondescdigestdistributionaldplyrfansifarverfuturefuture.applygenericsggplot2ggridgesglobalsgluegridExtragtablehmsinlineisobandlabelinglatticelifecyclelistenvlme4loomagrittrMASSMatrixmatrixStatsmgcvminqamunsellmvtnormnleqslvnlmenloptrnumDerivparallellypillarpkgbuildpkgconfigplyrposteriorprettyunitsprocessxprogresspsQuickJSRR6RColorBrewerRcppRcppEigenRcppParallelreshape2rlangrstanrstantoolsscalesStanHeadersstringistringrtensorAtibbletidyselectutf8vctrsviridisLitewithr